The emergence of diffusion weighted imaging (DWI) and diffusion tensor imaging (DTI) provides a means via water diffusion to investigate the white matter integrity in the human brain and its impact on neuronal functions. Quantitative mapping of tissue diffusion properties, such as the apparent diffusion coefficient (ADC) and fractional anisotropy (FA) derived from DWI and DTI scans, is sensitive to the pathological changes in various diseases, and is therefore clinically valuable. The most successful application of the ADC mapping since the late 1980s and the early 1990s has been brain ischemia. For example, in 1990, Moseley et al. showed that the brain diffusion coefficient drops at a very early stage of the ischemic event, and in 1992, Chien et al. and Warach et al. showed that ADC mapping is clinically valuable in detecting early pathological changes in stroke patients. Since then the ADC mapping has been used in numerous stroke studies and its clinical value has been established. In 1994, Basser reported that the FA maps derived from DTI provide unique information on white matter integrity, and in 1996, Pierpaoli et al. showed that FA mapping is clinically valuable, particularly for improving the neuroradiologic assessment of a variety of white matter disorders. Since then, DTI has been widely used to assess white matter development and pathology. In order to improve the signal-to-noise ratio and reduce potential motion-related artifacts, human DWI and DTI data are usually acquired with partial Fourier echo-planar imaging (EPI). However, partial-Fourier EPI based DWI and DTI are susceptible to unique Type 1 and Type 2 artifacts as discussed in Chen et al., Improved image reconstruction for partial fourier gradient-echo echo-planar imaging (EPI), Magnetic Resonance in Medicine 2008; 59; 916-924, and other types of artifact such as geometric distortions resulting from eddy current effect and field inhomogeneities. The artifacts may cause quantitative inaccuracies in MRI data acquired with conventional DWI and DTI protocols.